[Bioc-devel] unable to push local changes to bioconductor svn repository

[Malgorzata Nowicka]

Hello, 

I have followed Scenario number 2 for my svn mirror for the cytofWorkflow package (more precisely workflow) and I encounter the same problem as described below by Zongli. 

Below are my exact steps. The same steps worked for my other package DRIMSeq.

Could it be because it is a workflow and not a regular package? If I do not change the update_remotes.sh file, there are even more errors because cytofWorkflow is not at https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ <https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/>.

How should I fix it?

Thank you for your help,

Gosia


### I have forked https://github.com/Bioconductor-mirror/cytofWorkflow <https://github.com/Bioconductor-mirror/cytofWorkflow> to my repo https://github.com/gosianow/cytofWorkflow.git <https://github.com/gosianow/cytofWorkflow.git>
### I have added a commit to https://github.com/gosianow/cytofWorkflow.git <https://github.com/gosianow/cytofWorkflow.git>
### Now, I would like to update the bioc svn

$ git clone https://github.com/gosianow/cytofWorkflow.git <https://github.com/gosianow/cytofWorkflow.git>

$ curl -O https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh <https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh>

$ cd cytofWorkflow

### Replace Rpacks with workflows in update_remotes.sh as cytofWorkflow is in https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/ <https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow/>

$ bash ../update_remotes.sh

$ git branch -a

$ git checkout devel

$ git svn rebase

Migrating from a git-svn v1 layout...
Data from a previous version of git-svn exists, but
	.git/svn
	(required for this version (2.11.0 (Apple Git-81)) of git-svn) does not exist.
Done migrating from a git-svn v1 layout
Unable to determine upstream SVN information from working tree history



> On 12 May 2017, at 15:52, Martin Morgan <martin.morgan at roswellpark.org> wrote:
> 
> On 05/11/2017 10:02 AM, Xu, Zongli (NIH/NIEHS) [E] wrote:
>> Hi,
>> 
>> 
>> 
>> I got a new Linux computer, cloned my package from github, made some
>> changes. I am able to update the changes to github, but can not push
>> it to Bioconductor svn repository. Can someone help me to solve the
>> problem.
>> 
>> 
>> 
>> The following is what I did:
>> 
>> 
>> 
>> git svn clone https://github.com/xuz1/ENmix
> 
> The github repository is just a git repository, not SVN; you should follow the directions at scenario 2 of
> 
>  http://bioconductor.org/developers/how-to/git-mirrors/ <http://bioconductor.org/developers/how-to/git-mirrors/>
> 
> checkout the git repository, add svn remotes, rebase with svn, make git commits, then dcommit to svn.
> 
> Martin
> 
> 
>> 
>> cd ENmix
>> 
>> bash ../update_remotes.sh
>> 
>> 
>> 
>> #push to github
>> 
>> git checkout master
>> 
>> git add -A .
>> 
>> git commit -a -s -m "commit made by Xu"
>> 
>> git remote -v
>> 
>> git push origin master
>> 
>> 
>> 
>> #push to Bioconductor svn
>> 
>> git checkout devel
>> 
>> 
>> 
>> I am good up to here, but when I run the following command
>> 
>> git svn rebase --username  z.xu
>> 
>> 
>> 
>> It showed the following error message:
>> 
>> 
>> 
>> Data from a previous version of git-svn exists, but
>> 
>> .git/svn
>> 
>> (required for this version (1.7.1) of git-svn) does not exist.
>> 
>> Done migrating from a git-svn v1 layout
>> 
>> Unable to determine upstream SVN information from working tree
>> history
>> 
>> 
>> 
>> Can anyone guide me what should I do to solve this problem.
>> 
>> 
>> 
>> Thanks,
>> 
>> Zongli
>> 
>> [[alternative HTML version deleted]]
>> 
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
> 
> This email message may contain legally privileged and/or...{{dropped:2}}
> 
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